## Models

**Navigation**

Below is displayed the **model view** of the selected project. Model view is shown in the form of the model overview page for the currently selected model. The central feature of the model view is the model scheme that shows individual model components of selected model. The navigation panel on the left allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.

**Annotations Tab**

All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.

**Components Tab**

The Components Tab displays all the model species (state variables). More information for particular components are accessible after clicking on the requested component header.

**Reactions Tab**

Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.

**Parameters Tab**

All quantitative parameters are managed under Parameters Tab. Constants are separated from assigned quantities.

**Simulation Tab**

Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of initial conditions, parameters, options and datasets are listed in respective folders.

**Analysis Tab**

Conservation analysis, modes analysis and matrix analysis are available by clicking on appropriate buttons.

**Experiments Tab**

Experiments tab contains list of all experiments related to selected model.

## Müller et al. 2017 (in prep)

A mathematical model of carbon fluxes in a laboratory scale photobioreactor (gas/liquid CO_{2 }transfer, carbonate chemistry, and cellular exchange).

Here we provide an integrative model of carbon fluxes in a laboratory scale photobioreactor (gas/liquid CO_{2} transfer, carbonate chemistry, and cellular exchange). Starting from a detailed dynamic model with many unknown parameters, we eliminate fast time scales and obtain a reduced model containing only parameters available from independent experiments. The model allows to determine all CO_{2} related exchange rates of a photosynthetic culture, to reason about the internal mechanisms of carbon fixation, and to estimate maximum production rates of biomass or biofuels. To this end, the model has to be integrated with minimal cell models of phototrophic microorganisms, which are developed in parallel. Further, the model can be part of an advanced tool for the design and upscaling of bioreactors to industrial level.

**model: Mueller et al. (2016)**

**Contains:**

**Equation:**dCO2 -> HCO3_m

**Function:**Mass Action (reversible)

**Reaction rate:**k1_m_f*OH_m * dCO2-k1_m_b*HCO3_m

Kinetic rate constant | Value |
---|---|

k1_m_b |
9.71e-5*3600 |

k1_m_f |
2.23e+3*3600 |

**Equation:**dCO2 -> HCO3_m

**Function:**Mass Action (reversible)

**Reaction rate:**k1_p_f*dCO2-k1_p_b*H_p * HCO3_m

Kinetic rate constant | Value |
---|---|

k1_p_b |
2.67e+4*3600 |

k1_p_f |
3.71e-2*3600 |

**Equation:**HCO3_m -> CO3_2m

**Function:**Mass Action (reversible)

**Reaction rate:**k2_m_f*OH_m * HCO3_m-k2_m_b*CO3_2m

Kinetic rate constant | Value |
---|---|

k2_m_b |
3.06e+5*3600 |

k2_m_f |
6e+9*3600 |

**Equation:**HCO3_m -> CO3_2m

**Function:**Mass Action (reversible)

**Reaction rate:**k2_p_f*HCO3_m-k2_p_b*H_p * CO3_2m

Kinetic rate constant | Value |
---|---|

k2_p_b |
5e+10*3600 |

k2_p_f |
59.44*3600 |

**Equation:**HA -> A_m

**Function:**Mass Action (reversible)

**Reaction rate:**kB_f*HA-kB_b*H_p * A_m

Kinetic rate constant | Value |
---|---|

kB_b |
500000000 |

kB_f |
15.81 |

**Equation:**-> H_p

**Function:**Constant influx, variable outflux (reversible)

**Reaction rate:**kW_f-kW_b*OH_m * H_p

Kinetic rate constant | Value |
---|---|

kW_b |
2 |

kW_f |
"KW"*"kW_b" |

**Equation:**-> dCO2

**Function:**General flux (reversible)

**Reaction rate:**q_CO2

Kinetic rate constant | Value |
---|---|

q_CO2 |
0 |

**Equation:**-> HCO3_m

**Function:**General flux (reversible)

**Reaction rate:**q_HCO3_m

Kinetic rate constant | Value |
---|---|

q_HCO3_m |
0 |

#### Constant quantities

**Initial expression:**0

**Simulation type:**fixed

**Initial expression:**0

**Simulation type:**fixed

**Initial expression:**29

**Simulation type:**fixed

**Initial expression:**0.03

**Simulation type:**fixed

**Initial expression:**1

**Simulation type:**fixed

**Initial expression:**5000

**Simulation type:**fixed

**Initial expression:**15.81

**Simulation type:**fixed

**Initial expression:**500000000

**Simulation type:**fixed

**Initial expression:**2

**Simulation type:**fixed

**Initial expression:**5e+10*3600

**Simulation type:**fixed

**Initial expression:**59.44*3600

**Simulation type:**fixed

**Initial expression:**3.06e+5*3600

**Simulation type:**fixed

**Initial expression:**6e+9*3600

**Simulation type:**fixed

**Initial expression:**9.71e-5*3600

**Simulation type:**fixed

**Initial expression:**2.23e+3*3600

**Simulation type:**fixed

**Initial expression:**2.67e+4*3600

**Simulation type:**fixed

**Initial expression:**3.71e-2*3600

**Simulation type:**fixed

**Initial expression:**1e-14

**Simulation type:**fixed

#### Assigned quantities

**Initial expression:**kH_cp*gCO2_in_ppm*P_in_atm/1e+6

**Simulation type:**assignment

**Initial expression:**KW*kW_b

**Simulation type:**assignment

M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI